[ARVADOS] updated: 840274689ad8b42e5c1e42e7df4ed4dce80b1666
git at public.curoverse.com
git at public.curoverse.com
Wed Aug 20 10:31:20 EDT 2014
Summary of changes:
doc/images/workbench-move-selected.png | Bin 0 -> 8602 bytes
doc/user/reference/api-tokens.html.textile.liquid | 2 +-
.../tutorials/tutorial-keep.html.textile.liquid | 6 +++++-
...tutorial-pipeline-workbench.html.textile.liquid | 22 ++++++++++-----------
4 files changed, 17 insertions(+), 13 deletions(-)
create mode 100644 doc/images/workbench-move-selected.png
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commit 840274689ad8b42e5c1e42e7df4ed4dce80b1666
Author: Brett Smith <brett at curoverse.com>
Date: Wed Aug 20 10:32:54 2014 -0400
3499: First round of review updates.
diff --git a/doc/images/workbench-move-selected.png b/doc/images/workbench-move-selected.png
new file mode 100644
index 0000000..351568a
Binary files /dev/null and b/doc/images/workbench-move-selected.png differ
diff --git a/doc/user/reference/api-tokens.html.textile.liquid b/doc/user/reference/api-tokens.html.textile.liquid
index 3e42984..768c7d1 100644
--- a/doc/user/reference/api-tokens.html.textile.liquid
+++ b/doc/user/reference/api-tokens.html.textile.liquid
@@ -10,7 +10,7 @@ Access the Arvados Workbench using this link: "https://{{ site.arvados_workbench
Open a shell on the system where you want to use the Arvados client. This may be your local workstation, or an Arvados virtual machine accessed with SSH (instructions for "Unix":{{site.baseurl}}/user/getting_started/ssh-access-unix.html#login or "Windows":{{site.baseurl}}/user/getting_started/ssh-access-windows.html#login).
-Click on the link with your _email address_ in the upper right corner to access the user settings menu, and click on the menu item *Manage account* to go to the account management page. On the *Manage account* page, you will see the *Current Token* panel, which lists your current token and instructions to set up your environment.
+Click on the link with your _email address_ in the upper right corner to access your account menu, then click on the menu item *Manage account* to go to the account management page. On the *Manage account* page, you will see the *Current Token* panel, which lists your current token and instructions to set up your environment.
h2. Setting environment variables
diff --git a/doc/user/tutorials/tutorial-keep.html.textile.liquid b/doc/user/tutorials/tutorial-keep.html.textile.liquid
index 0c45366..74319fd 100644
--- a/doc/user/tutorials/tutorial-keep.html.textile.liquid
+++ b/doc/user/tutorials/tutorial-keep.html.textile.liquid
@@ -28,7 +28,11 @@ c1bad4b39ca5a924e481008009d94e32+210
* The output value @c1bad4b39ca5a924e481008009d94e32+210@ is the Arvados collection locator that uniquely describes this file.
-Now visit the Workbench *Dashboard*. In the *My projects* pane, select your *Home* project. Your newly uploaded collection should appear near the top of the *Data collections* tab. The collection locator printed by @arv-put@ will appear under the *name* column. To move the collection to a specific project, check the box at the left of the collection row. Pull down the *Selection...* menu near the top of the page tab, and select *Move selected*. This will open a dialog box where you can select a destination project for the collection. Click a project, then finally the <span class="btn btn-sm btn-primary">Move</span> button.
+Now visit the Workbench *Dashboard*. In the *My projects* pane, select your *Home* project. Your newly uploaded collection should appear near the top of the *Data collections* tab. The collection locator printed by @arv-put@ will appear under the *name* column. To move the collection to a different project, check the box at the left of the collection row. Pull down the *Selection...* menu near the top of the page tab, and select *Move selected*.
+
+!{{ site.baseurl }}/images/workbench-move-selected.png!
+
+This will open a dialog box where you can select a destination project for the collection. Click a project, then finally the <span class="btn btn-sm btn-primary">Move</span> button.
Click on the *<i class="fa fa-fw fa-archive"></i> Show* button next to the collection's listing on a project page to go to the Workbench page for your collection. On this page, you can see the collection's contents, download individual files, and set sharing options.
diff --git a/doc/user/tutorials/tutorial-pipeline-workbench.html.textile.liquid b/doc/user/tutorials/tutorial-pipeline-workbench.html.textile.liquid
index 3cc8487..5df82a7 100644
--- a/doc/user/tutorials/tutorial-pipeline-workbench.html.textile.liquid
+++ b/doc/user/tutorials/tutorial-pipeline-workbench.html.textile.liquid
@@ -4,7 +4,7 @@ navsection: userguide
title: "Running a pipeline using Workbench"
...
-A "pipeline" (sometimes called a "workflow" in other systems) is sequence of steps that apply various programs or tools to transform input data to output data. Pipelines are the principal means of performing computation with Arvados. This tutorial demonstrates how to run a single-stage pipeline to take a small data set of paired-end reads from an sample "exome":https://en.wikipedia.org/wiki/Exome in "FASTQ":https://en.wikipedia.org/wiki/FASTQ_format format and align them to "Chromosome 19":https://en.wikipedia.org/wiki/Chromosome_19_%28human%29 using the "bwa mem":http://bio-bwa.sourceforge.net/ tool, producing a "Sequence Alignment/Map (SAM)":https://samtools.github.io/ file. This will introduce the following Arvados features:
+A "pipeline" (sometimes called a "workflow" in other systems) is a sequence of steps that apply various programs or tools to transform input data to output data. Pipelines are the principal means of performing computation with Arvados. This tutorial demonstrates how to run a single-stage pipeline to take a small data set of paired-end reads from a sample "exome":https://en.wikipedia.org/wiki/Exome in "FASTQ":https://en.wikipedia.org/wiki/FASTQ_format format and align them to "Chromosome 19":https://en.wikipedia.org/wiki/Chromosome_19_%28human%29 using the "bwa mem":http://bio-bwa.sourceforge.net/ tool, producing a "Sequence Alignment/Map (SAM)":https://samtools.github.io/ file. This will introduce the following Arvados features:
<div class="inside-list">
* How to create a project.
@@ -15,18 +15,18 @@ A "pipeline" (sometimes called a "workflow" in other systems) is sequence of ste
notextile. <div class="spaced-out">
-# Start from the *Workbench Dashboard*. You can return to the Dashboard by clicking on *<i class="fa fa-lg fa-fw fa-dashboard"></i> Dashboard* in the upper left corner of any Workbench page.
-# On the *My projects* panel, click <span class="btn btn-sm btn-primary" > <i class="fa fa-fw fa-plus"></i> Add new project</span>. This will direct you to the page for the new project.
-# On the new project page, click on the pencil icon <i class="fa fa-fw fa-pencil"></i> next to *New project* to pop up a text box and change the project title to *Tutorial output*. Click the checkbox <span class="btn btn-xs btn-primary" ><i class="glyphicon glyphicon-ok"></i></span> to save the new name.
-# Click on <span class="btn btn-sm btn-primary"><i class="fa fa-fw fa-gear"></i> Run a pipeline...</span> This will open a dialog box titled *Choose a pipeline to run*.
-# Click on *All projects <span class="caret"></span>*. Under the *Projects shared with me* header, select *<i class="fa fa-fw fa-share-alt"></i> Arvados Tutorial*.
-# Select *<i class="fa fa-fw fa-gear"></i> Tutorial align using bwa mem* and click on <span class="btn btn-sm btn-primary" >Next: choose inputs <i class="fa fa-fw fa-arrow-circle-right"></i></span>. This will load a new page where you will supply the inputs for the pipeline.
+# Start from the *Workbench Dashboard*. You can access the Dashboard by clicking on *<i class="fa fa-lg fa-fw fa-dashboard"></i> Dashboard* in the upper left corner of any Workbench page.
+# In the *My projects* panel, click the <span class="btn btn-sm btn-primary" > <i class="fa fa-fw fa-plus"></i> Add new project</span> button. The new project will be created immediately, and your browser opens the new project's page for you to customize it.
+# On the new project page, click on the pencil icon <i class="fa fa-fw fa-pencil"></i> next to *New project* to pop up a text box and change the project title to *Tutorial output*. Click the <span class="btn btn-xs btn-primary" ><i class="glyphicon glyphicon-ok"></i></span> checkbox button to save the new name.
+# Click on the <span class="btn btn-sm btn-primary"><i class="fa fa-fw fa-gear"></i> Run a pipeline...</span> button. This will open a dialog box titled *Choose a pipeline to run*.
+# Click to open the *All projects <span class="caret"></span>* menu. Under the *Projects shared with me* header, select *<i class="fa fa-fw fa-share-alt"></i> Arvados Tutorial*.
+# Select *<i class="fa fa-fw fa-gear"></i> Tutorial align using bwa mem* and click the <span class="btn btn-sm btn-primary" >Next: choose inputs <i class="fa fa-fw fa-arrow-circle-right"></i></span> button. This will load a new page where you will supply the inputs for the pipeline.
# The first input parameter to the pipeline is *Reference genoma (fasta)*. Click the <span class="btn btn-sm btn-primary">Choose</span> button beneath that header. This will open a dialog box titled *Choose a dataset for Reference genome (fasta)*.
-# Once again, open the *All projects <span class="caret"></span>* menu and select *<i class="fa fa-fw fa-share-alt"></i> Arvados Tutorial*. Select *<i class="fa fa-fw fa-archive"></i> Tutorial chromosome 19 reference* and click <span class="btn btn-sm btn-primary" >OK</span>.
+# Once again, open the *All projects <span class="caret"></span>* menu and select *<i class="fa fa-fw fa-share-alt"></i> Arvados Tutorial*. Select *<i class="fa fa-fw fa-archive"></i> Tutorial chromosome 19 reference* and click the <span class="btn btn-sm btn-primary" >OK</span> button.
# Repeat the previous two steps to set the *Input genome (fastq)* parameter to *<i class="fa fa-fw fa-archive"></i> Tutorial sample exome*.
-# Click on <span class="btn btn-sm btn-primary" >Run <i class="fa fa-fw fa-play"></i></span>. The page updates to show you that the pipeline has been submitted to run on the Arvados cluster.
-# After the pipeline starts running, you can track the progress by watching log messages from jobs. This page refreshes automatically. You will see <span class="label label-success">success</span> under the *job* the column when the pipeline completes successfully.
+# Click on the <span class="btn btn-sm btn-primary" >Run <i class="fa fa-fw fa-play"></i></span> button. The page updates to show you that the pipeline has been submitted to run on the Arvados cluster.
+# After the pipeline starts running, you can track the progress by watching log messages from jobs. This page refreshes automatically. You will see a <span class="label label-success">success</span> label under the *job* the column when the pipeline completes successfully.
# Click on *<i class="fa fa-fw fa-archive"></i> Show output files* to see the results of the job. This will load a new page listing the output files from this pipeline. You'll see the output SAM file from the alignment tool under the *Files* tab.
-# Click on the download button <span class="btn btn-sm btn-info"><i class="fa fa-download"></i></span> to the right of the SAM file download your results.
+# Click on the <span class="btn btn-sm btn-info"><i class="fa fa-download"></i></span> download button to the right of the SAM file to download your results.
notextile. </div>
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